Systems Biology Model Validation & Simulation Tools — Hands-on

Learn how to verify, validate and simulate systems biology models so they are trustworthy and reusable. This module focuses on basic verification checks, validation against data, uncertainty and sensitivity views, and practical use of SBML friendly simulation tools to run time course, steady state and scenario analyses with clear reporting.

Systems Biology Model Validation & Simulation Tools

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Session Index

Session 1 — Model Verification & Validation Foundations Session 2 — Simulation Tools & SBML Workflows Session 3 — Parameter Scans, Sensitivity & Scenarios Session 4 — Mini Capstone: Model Validation & Simulation Report

Session 1

Fee: Rs 8800

Model Verification & Validation Foundations

What it means for a systems biology model to be “valid”

concepts of verification vs validation structural checks and consistency qualitative vs quantitative agreement

Common issues in models and how to spot them early

units, parameter ranges and sign errors mass balance and conservation ideas nonphysical trajectories and instability

Toolchain for basic model checks and documentation

SBML style representations (concept level) simple scripts for sanity checks model metadata and version notes

Session 2

Fee: Rs 11800

Simulation Tools & SBML Workflows

Overview of simulation environments for systems models

visual model editors (concept view) SBML compatible solvers and GUIs scriptable simulation via R / Python

Setting up time course and steady state simulations

initial conditions and parameter sets step sizes and solver options overview saving trajectories and outputs cleanly

Implementation toolkit for SBML centric workflows

import / export between editors and code simple scripts to batch run simulations organising simulation projects and files

Session 3

Fee: Rs 14800

Parameter Scans, Sensitivity & Scenarios

Exploring parameter space with scans and grids

one at a time parameter sweeps coarse grid exploration ideas summaries of output ranges and behaviours

Sensitivity and basic uncertainty views (concept level)

local sensitivity around a reference set simple global style sampling ideas heatmaps and summary indices

Implementation toolkit for scans and scenario management

scripts for looped simulations R / Python plotting of parameter vs outputs scenario naming and comparison tables

Session 4

Fee: Rs 18800

Mini Capstone: Model Validation & Simulation Report

Design a small validation and simulation plan for a model

Theory + Practical

Run simulations, parameter scans and summarise model behaviour

baseline and perturbed runs figures for key trajectories simple validation statements vs expectations

Deliverables: notebook, simulation outputs & validation summary

R or Python simulation notebook CSV/TSV output tables and figures PDF/HTML model validation report

PDF

Systems Biology Model Validation & Simulation Tools Training | SBML Workflows, Scans & Validation

Systems Biology Model Validation & Simulation Tools — Hands-on